Starting phenix.real_space_refine
on Wed Mar  5 22:05:00 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8wx5_37901/03_2025/8wx5_37901.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wx5_37901/03_2025/8wx5_37901.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wx5_37901/03_2025/8wx5_37901.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wx5_37901/03_2025/8wx5_37901.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wx5_37901/03_2025/8wx5_37901.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wx5_37901/03_2025/8wx5_37901.cif"
  }
  resolution = 3.91
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.052
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    2552      2.51       5
     N     619      2.21       5
     O     664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3857
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 490, 3741
          Classifications: {'peptide': 490}
          Link IDs: {'PTRANS': 22, 'TRANS': 467}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 116
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
  Time building chain proxies: 2.92, per 1000 atoms: 0.76
  Number of scatterers: 3857
  At special positions: 0
  Unit cell: (80.51, 77.19, 73.87, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      22     16.00
     O     664      8.00
     N     619      7.00
     C    2552      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 153 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 141 " - pdb=" SG  CYS A 152 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 489.8 milliseconds
  

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  922

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 1 sheets defined
      83.7% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 57
      removed outlier: 3.927A  pdb=" N   ASN A  57 " --> pdb=" O   GLY A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 65
      removed outlier: 3.539A  pdb=" N   ASN A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 97
      Proline residue:  A  90  - end of helix
    Processing helix  chain 'A' and resid 101 through 125
      Proline residue:  A 121  - end of helix
    Processing helix  chain 'A' and resid 125 through 134
    Processing helix  chain 'A' and resid 146 through 185
      removed outlier: 3.514A  pdb=" N   ALA A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
      Proline residue:  A 155  - end of helix
      removed outlier: 4.443A  pdb=" N   THR A 176 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
      Proline residue:  A 177  - end of helix
      removed outlier: 4.049A  pdb=" N   ASP A 185 " --> pdb=" O   ASP A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 220
    Processing helix  chain 'A' and resid 221 through 245
      Proline residue:  A 229  - end of helix
      removed outlier: 4.111A  pdb=" N   SER A 245 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 268
    Processing helix  chain 'A' and resid 310 through 349
      Proline residue:  A 323  - end of helix
      Proline residue:  A 330  - end of helix
    Processing helix  chain 'A' and resid 354 through 358
      removed outlier: 4.283A  pdb=" N   ILE A 357 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 394
      Proline residue:  A 382  - end of helix
      Proline residue:  A 390  - end of helix
      removed outlier: 3.897A  pdb=" N   ARG A 394 " --> pdb=" O   PRO A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 431
    Processing helix  chain 'A' and resid 450 through 452
      No H-bonds generated for 'chain 'A' and resid 450 through 452'
    Processing helix  chain 'A' and resid 453 through 479
      removed outlier: 4.550A  pdb=" N   GLN A 457 " --> pdb=" O   TRP A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 512
    Processing helix  chain 'A' and resid 526 through 530
    Processing helix  chain 'A' and resid 531 through 556
      removed outlier: 4.067A  pdb=" N   TYR A 535 " --> pdb=" O   TYR A 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 14
    Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 437
      removed outlier: 3.715A  pdb=" N   GLN A 437 " --> pdb=" O   TYR A 444 " (cutoff:3.500A)

    315 hydrogen bonds defined for protein.
    930 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.09

  Time building geometry restraints manager: 1.11 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.18 -     1.31: 588
        1.31 -     1.43: 1104
        1.43 -     1.56: 2230
        1.56 -     1.69: 0
        1.69 -     1.82: 33
  Bond restraints: 3955
  Sorted by residual:
  bond pdb=" C   SER B   8 "
       pdb=" O   SER B   8 "
    ideal  model  delta    sigma   weight residual
    1.236  1.307 -0.070 1.24e-02 6.50e+03 3.21e+01
  bond pdb=" C   LEU B   7 "
       pdb=" O   LEU B   7 "
    ideal  model  delta    sigma   weight residual
    1.236  1.294 -0.058 1.19e-02 7.06e+03 2.34e+01
  bond pdb=" CA  SER B   8 "
       pdb=" CB  SER B   8 "
    ideal  model  delta    sigma   weight residual
    1.530  1.452  0.078 1.69e-02 3.50e+03 2.11e+01
  bond pdb=" C   TYR B   6 "
       pdb=" O   TYR B   6 "
    ideal  model  delta    sigma   weight residual
    1.235  1.181  0.054 1.26e-02 6.30e+03 1.84e+01
  bond pdb=" C   GLY B   9 "
       pdb=" O   GLY B   9 "
    ideal  model  delta    sigma   weight residual
    1.235  1.179  0.056 1.35e-02 5.49e+03 1.72e+01
  ... (remaining 3950 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 5238
        2.18 -     4.37: 114
        4.37 -     6.55: 23
        6.55 -     8.73: 5
        8.73 -    10.92: 4
  Bond angle restraints: 5384
  Sorted by residual:
  angle pdb=" N   GLU B   4 "
        pdb=" CA  GLU B   4 "
        pdb=" C   GLU B   4 "
      ideal   model   delta    sigma   weight residual
     112.34  102.39    9.95 1.30e+00 5.92e-01 5.86e+01
  angle pdb=" N   LEU B  10 "
        pdb=" CA  LEU B  10 "
        pdb=" C   LEU B  10 "
      ideal   model   delta    sigma   weight residual
     111.37  100.45   10.92 1.64e+00 3.72e-01 4.43e+01
  angle pdb=" N   TRP B  13 "
        pdb=" CA  TRP B  13 "
        pdb=" C   TRP B  13 "
      ideal   model   delta    sigma   weight residual
     111.37  102.04    9.33 1.65e+00 3.67e-01 3.20e+01
  angle pdb=" N   SER B   8 "
        pdb=" CA  SER B   8 "
        pdb=" C   SER B   8 "
      ideal   model   delta    sigma   weight residual
     111.75  104.52    7.23 1.28e+00 6.10e-01 3.19e+01
  angle pdb=" N   TYR B  12 "
        pdb=" CA  TYR B  12 "
        pdb=" C   TYR B  12 "
      ideal   model   delta    sigma   weight residual
     111.36  117.06   -5.70 1.09e+00 8.42e-01 2.73e+01
  ... (remaining 5379 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 2037
       17.98 -    35.95: 206
       35.95 -    53.93: 43
       53.93 -    71.91: 3
       71.91 -    89.89: 2
  Dihedral angle restraints: 2291
    sinusoidal: 849
      harmonic: 1442
  Sorted by residual:
  dihedral pdb=" N   SER B   8 "
           pdb=" C   SER B   8 "
           pdb=" CA  SER B   8 "
           pdb=" CB  SER B   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  112.32   10.48     0      2.50e+00 1.60e-01 1.76e+01
  dihedral pdb=" N   LEU B  10 "
           pdb=" C   LEU B  10 "
           pdb=" CA  LEU B  10 "
           pdb=" CB  LEU B  10 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  112.37   10.43     0      2.50e+00 1.60e-01 1.74e+01
  dihedral pdb=" C   TRP B  13 "
           pdb=" N   TRP B  13 "
           pdb=" CA  TRP B  13 "
           pdb=" CB  TRP B  13 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.16   -9.44     0      2.50e+00 1.60e-01 1.42e+01
  ... (remaining 2288 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 564
       0.064 -    0.128: 57
       0.128 -    0.192: 3
       0.192 -    0.256: 1
       0.256 -    0.319: 3
  Chirality restraints: 628
  Sorted by residual:
  chirality pdb=" CA  TRP B  13 "
            pdb=" N   TRP B  13 "
            pdb=" C   TRP B  13 "
            pdb=" CB  TRP B  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.55e+00
  chirality pdb=" CA  TYR B  12 "
            pdb=" N   TYR B  12 "
            pdb=" C   TYR B  12 "
            pdb=" CB  TYR B  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CA  LEU B  10 "
            pdb=" N   LEU B  10 "
            pdb=" C   LEU B  10 "
            pdb=" CB  LEU B  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.05e+00
  ... (remaining 625 not shown)

  Planarity restraints: 664
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B   9 "    0.020 2.00e-02 2.50e+03   4.12e-02 1.70e+01
        pdb=" C   GLY B   9 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   GLY B   9 "    0.027 2.00e-02 2.50e+03
        pdb=" N   LEU B  10 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  10 "    0.013 2.00e-02 2.50e+03   2.64e-02 6.99e+00
        pdb=" C   LEU B  10 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   LEU B  10 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLU B  11 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 228 "   -0.034 5.00e-02 4.00e+02   5.13e-02 4.21e+00
        pdb=" N   PRO A 229 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 229 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 229 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 661 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 215
        2.73 -     3.27: 4249
        3.27 -     3.81: 6741
        3.81 -     4.36: 7416
        4.36 -     4.90: 12796
  Nonbonded interactions: 31417
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 349 "
            pdb=" NE2 GLN A 437 "
     model   vdw
     2.184 3.120
  nonbonded pdb=" O   GLN A 337 "
            pdb=" OG1 THR A 341 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG  SER A 355 "
            pdb=" O   THR A 358 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG1 THR A 333 "
            pdb=" O   GLY A 499 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   LEU A 380 "
            pdb=" N   LYS A 384 "
     model   vdw
     2.280 3.120
  ... (remaining 31412 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.780
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   3955  Z= 0.255
  Angle     :  0.867  10.916   5384  Z= 0.555
  Chirality :  0.044   0.319    628
  Planarity :  0.005   0.051    664
  Dihedral  : 14.579  89.886   1363
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  6.63 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  6.98 %
    Favored  : 92.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.34), residues: 498
  helix: -0.26 (0.24), residues: 389
  sheet: -4.91 (0.87), residues: 10
  loop : -4.00 (0.45), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP B  13 
 HIS   0.002   0.000   HIS A 362 
 PHE   0.012   0.001   PHE A  67 
 TYR   0.022   0.002   TYR B  12 
 ARG   0.001   0.000   ARG A 102 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 157
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 LEU cc_start: 0.9316 (mt) cc_final: 0.9044 (mt)
REVERT: A   63 ASN cc_start: 0.7813 (m110) cc_final: 0.7512 (t0)
REVERT: A  259 ASP cc_start: 0.9094 (m-30) cc_final: 0.8872 (m-30)
REVERT: A  310 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8282 (mm-30)
REVERT: A  409 MET cc_start: 0.9073 (mtt) cc_final: 0.8799 (mtt)
REVERT: A  453 TRP cc_start: 0.7998 (m100) cc_final: 0.7208 (m100)
REVERT: A  465 GLU cc_start: 0.9358 (tp30) cc_final: 0.9097 (tp30)
REVERT: A  470 ILE cc_start: 0.8834 (mm) cc_final: 0.8583 (mm)
REVERT: A  474 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7222 (mt-10)
  outliers start: 2
  outliers final: 1
  residues processed: 158
  average time/residue: 0.1313
  time to fit residues: 26.3633
Evaluate side-chains
  129 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 12 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0870
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.5758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 GLN
A 356 ASN
A 441 ASN
A 454 GLN
B  14 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.149047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.124815 restraints weight = 7523.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.128568 restraints weight = 4284.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.131091 restraints weight = 2885.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3955  Z= 0.195
  Angle     :  0.656   7.811   5384  Z= 0.335
  Chirality :  0.041   0.161    628
  Planarity :  0.005   0.052    664
  Dihedral  :  4.704  16.291    538
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 16.46 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.38), residues: 498
  helix:  0.81 (0.26), residues: 390
  sheet:  None (None), residues: 0
  loop : -3.29 (0.50), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  13 
 HIS   0.003   0.001   HIS A 348 
 PHE   0.018   0.001   PHE A 194 
 TYR   0.034   0.002   TYR B  12 
 ARG   0.008   0.000   ARG A 426 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 LEU cc_start: 0.9518 (mt) cc_final: 0.9114 (mp)
REVERT: A  120 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8391 (t80)
REVERT: A  240 PHE cc_start: 0.9111 (t80) cc_final: 0.8900 (t80)
REVERT: A  259 ASP cc_start: 0.9113 (m-30) cc_final: 0.8905 (m-30)
REVERT: A  409 MET cc_start: 0.9134 (mtt) cc_final: 0.8736 (mtt)
REVERT: A  423 GLU cc_start: 0.8505 (tp30) cc_final: 0.8155 (tp30)
REVERT: A  426 ARG cc_start: 0.8796 (ttp80) cc_final: 0.8396 (ttp80)
REVERT: A  453 TRP cc_start: 0.8070 (m100) cc_final: 0.7406 (m100)
REVERT: A  465 GLU cc_start: 0.9397 (tp30) cc_final: 0.8976 (tp30)
REVERT: A  470 ILE cc_start: 0.8745 (mm) cc_final: 0.8483 (mm)
REVERT: A  474 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7321 (mt-10)
REVERT: A  501 PHE cc_start: 0.8636 (m-80) cc_final: 0.7562 (t80)
REVERT: A  543 GLN cc_start: 0.9519 (tp40) cc_final: 0.9015 (tp-100)
REVERT: B   13 TRP cc_start: 0.5782 (OUTLIER) cc_final: 0.4622 (t-100)
  outliers start: 16
  outliers final: 8
  residues processed: 147
  average time/residue: 0.1146
  time to fit residues: 22.0580
Evaluate side-chains
  136 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0170
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.6818

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.145771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.122325 restraints weight = 7416.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.125843 restraints weight = 4222.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.128337 restraints weight = 2840.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3955  Z= 0.209
  Angle     :  0.658   8.109   5384  Z= 0.337
  Chirality :  0.042   0.166    628
  Planarity :  0.005   0.066    664
  Dihedral  :  4.644  16.497    537
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 20.95 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.39), residues: 498
  helix:  1.02 (0.26), residues: 396
  sheet:  None (None), residues: 0
  loop : -2.82 (0.57), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  13 
 HIS   0.001   0.001   HIS A 348 
 PHE   0.011   0.001   PHE A 195 
 TYR   0.027   0.002   TYR B  12 
 ARG   0.005   0.000   ARG A 129 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 TRP cc_start: 0.8983 (m-10) cc_final: 0.8600 (m-10)
REVERT: A  120 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8014 (t80)
REVERT: A  259 ASP cc_start: 0.9143 (m-30) cc_final: 0.8938 (m-30)
REVERT: A  423 GLU cc_start: 0.8462 (tp30) cc_final: 0.8091 (tp30)
REVERT: A  453 TRP cc_start: 0.8077 (m100) cc_final: 0.7393 (m100)
REVERT: A  465 GLU cc_start: 0.9334 (tp30) cc_final: 0.8972 (tp30)
REVERT: A  470 ILE cc_start: 0.8696 (mm) cc_final: 0.8401 (mm)
REVERT: A  474 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7358 (mt-10)
REVERT: A  501 PHE cc_start: 0.8651 (m-80) cc_final: 0.7628 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 134
  average time/residue: 0.1184
  time to fit residues: 20.7848
Evaluate side-chains
  135 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 36 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.143933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.120189 restraints weight = 7511.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.123698 restraints weight = 4291.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.126174 restraints weight = 2901.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3955  Z= 0.223
  Angle     :  0.650   9.044   5384  Z= 0.333
  Chirality :  0.041   0.134    628
  Planarity :  0.005   0.054    664
  Dihedral  :  4.559  17.188    537
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 25.44 %
    Favored  : 69.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.39), residues: 498
  helix:  1.13 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.62 (0.61), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  13 
 HIS   0.002   0.001   HIS A 348 
 PHE   0.010   0.001   PHE A 195 
 TYR   0.027   0.002   TYR B  12 
 ARG   0.004   0.000   ARG A 426 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 TRP cc_start: 0.7326 (m100) cc_final: 0.6990 (m100)
REVERT: A  203 ASN cc_start: 0.8719 (m-40) cc_final: 0.8371 (m-40)
REVERT: A  259 ASP cc_start: 0.9145 (m-30) cc_final: 0.8939 (m-30)
REVERT: A  316 LYS cc_start: 0.8888 (tttt) cc_final: 0.8666 (ttmt)
REVERT: A  423 GLU cc_start: 0.8501 (tp30) cc_final: 0.8291 (tp30)
REVERT: A  426 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8526 (ttp80)
REVERT: A  453 TRP cc_start: 0.8153 (m100) cc_final: 0.7500 (m100)
REVERT: A  465 GLU cc_start: 0.9319 (tp30) cc_final: 0.8996 (tp30)
REVERT: A  470 ILE cc_start: 0.8703 (mm) cc_final: 0.8376 (mm)
REVERT: A  474 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7351 (mt-10)
REVERT: A  501 PHE cc_start: 0.8682 (m-80) cc_final: 0.7708 (t80)
REVERT: B   13 TRP cc_start: 0.5859 (OUTLIER) cc_final: 0.5194 (m100)
  outliers start: 20
  outliers final: 13
  residues processed: 137
  average time/residue: 0.1093
  time to fit residues: 19.9184
Evaluate side-chains
  135 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  417 PHE
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0270
   chunk 48 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.6438

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.144124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.120369 restraints weight = 7647.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.123950 restraints weight = 4282.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.126536 restraints weight = 2839.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3955  Z= 0.205
  Angle     :  0.656   9.907   5384  Z= 0.332
  Chirality :  0.041   0.147    628
  Planarity :  0.005   0.051    664
  Dihedral  :  4.534  16.945    537
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 28.68 %
    Favored  : 66.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.39), residues: 498
  helix:  1.15 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.44 (0.63), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  13 
 HIS   0.001   0.000   HIS A 348 
 PHE   0.011   0.001   PHE A 194 
 TYR   0.024   0.002   TYR A 331 
 ARG   0.001   0.000   ARG A 426 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 TRP cc_start: 0.7308 (m100) cc_final: 0.7048 (m100)
REVERT: A  203 ASN cc_start: 0.8672 (m-40) cc_final: 0.8346 (m-40)
REVERT: A  423 GLU cc_start: 0.8485 (tp30) cc_final: 0.8216 (tp30)
REVERT: A  426 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8521 (ttp80)
REVERT: A  453 TRP cc_start: 0.8124 (m100) cc_final: 0.7467 (m100)
REVERT: A  465 GLU cc_start: 0.9285 (tp30) cc_final: 0.9017 (tp30)
REVERT: A  470 ILE cc_start: 0.8653 (mm) cc_final: 0.8326 (mm)
REVERT: A  474 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7390 (mt-10)
REVERT: A  501 PHE cc_start: 0.8688 (m-80) cc_final: 0.7724 (t80)
REVERT: B   13 TRP cc_start: 0.5706 (OUTLIER) cc_final: 0.5158 (m100)
  outliers start: 18
  outliers final: 14
  residues processed: 132
  average time/residue: 0.1238
  time to fit residues: 21.8864
Evaluate side-chains
  135 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.143029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.118558 restraints weight = 7635.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.122071 restraints weight = 4324.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.124468 restraints weight = 2919.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3955  Z= 0.216
  Angle     :  0.664  10.926   5384  Z= 0.337
  Chirality :  0.041   0.134    628
  Planarity :  0.005   0.046    664
  Dihedral  :  4.515  17.470    537
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 29.68 %
    Favored  : 66.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.39), residues: 498
  helix:  1.19 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.39 (0.63), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  13 
 HIS   0.002   0.001   HIS A 348 
 PHE   0.010   0.001   PHE A 411 
 TYR   0.022   0.002   TYR B  12 
 ARG   0.001   0.000   ARG A 129 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 GLU cc_start: 0.8542 (tp30) cc_final: 0.8273 (tp30)
REVERT: A  426 ARG cc_start: 0.8853 (ttp80) cc_final: 0.8548 (ttp80)
REVERT: A  453 TRP cc_start: 0.8206 (m100) cc_final: 0.7540 (m100)
REVERT: A  465 GLU cc_start: 0.9293 (tp30) cc_final: 0.9037 (tp30)
REVERT: A  470 ILE cc_start: 0.8656 (mm) cc_final: 0.8386 (mm)
REVERT: A  474 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7400 (mt-10)
REVERT: A  501 PHE cc_start: 0.8701 (m-80) cc_final: 0.7731 (t80)
REVERT: B   13 TRP cc_start: 0.5663 (OUTLIER) cc_final: 0.5130 (m100)
  outliers start: 16
  outliers final: 12
  residues processed: 129
  average time/residue: 0.1206
  time to fit residues: 20.1797
Evaluate side-chains
  132 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 48 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0170
   chunk 21 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.6018

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.143431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.119819 restraints weight = 7569.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.123337 restraints weight = 4229.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.125870 restraints weight = 2814.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3955  Z= 0.205
  Angle     :  0.681  11.215   5384  Z= 0.340
  Chirality :  0.041   0.143    628
  Planarity :  0.005   0.044    664
  Dihedral  :  4.514  17.056    537
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 31.67 %
    Favored  : 64.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.39), residues: 498
  helix:  1.24 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.40 (0.64), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  13 
 HIS   0.001   0.000   HIS A 348 
 PHE   0.010   0.001   PHE A 411 
 TYR   0.021   0.002   TYR B  12 
 ARG   0.004   0.000   ARG A  48 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 TRP cc_start: 0.7321 (m100) cc_final: 0.7113 (m100)
REVERT: A  310 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8716 (mm-30)
REVERT: A  453 TRP cc_start: 0.8184 (m100) cc_final: 0.7525 (m100)
REVERT: A  470 ILE cc_start: 0.8635 (mm) cc_final: 0.8375 (mm)
REVERT: A  474 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7384 (mt-10)
REVERT: A  501 PHE cc_start: 0.8694 (m-80) cc_final: 0.7763 (t80)
REVERT: B   13 TRP cc_start: 0.5727 (OUTLIER) cc_final: 0.5261 (m100)
  outliers start: 15
  outliers final: 12
  residues processed: 133
  average time/residue: 0.1140
  time to fit residues: 20.4606
Evaluate side-chains
  131 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0980
   chunk 27 optimal weight:    0.5980
   chunk 45 optimal weight:    0.4980
   chunk 43 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.145620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.121013 restraints weight = 7559.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.124802 restraints weight = 4294.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.127284 restraints weight = 2884.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.3424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3955  Z= 0.209
  Angle     :  0.705  11.562   5384  Z= 0.352
  Chirality :  0.041   0.150    628
  Planarity :  0.005   0.043    664
  Dihedral  :  4.529  17.175    537
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 32.92 %
    Favored  : 64.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.39), residues: 498
  helix:  1.22 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.34 (0.64), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  13 
 HIS   0.002   0.000   HIS A 348 
 PHE   0.008   0.001   PHE A 336 
 TYR   0.024   0.002   TYR A 331 
 ARG   0.013   0.001   ARG A 426 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8753 (mm-30)
REVERT: A  453 TRP cc_start: 0.8190 (m100) cc_final: 0.7528 (m100)
REVERT: A  470 ILE cc_start: 0.8585 (mm) cc_final: 0.8277 (mm)
REVERT: A  474 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7383 (mt-10)
REVERT: A  501 PHE cc_start: 0.8698 (m-80) cc_final: 0.7753 (t80)
REVERT: B   13 TRP cc_start: 0.5709 (OUTLIER) cc_final: 0.5264 (m100)
  outliers start: 12
  outliers final: 11
  residues processed: 131
  average time/residue: 0.1011
  time to fit residues: 17.9940
Evaluate side-chains
  135 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 21 optimal weight:    0.3980
   chunk 39 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.145568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.120889 restraints weight = 7599.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.124725 restraints weight = 4292.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.127210 restraints weight = 2877.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3955  Z= 0.220
  Angle     :  0.725  12.154   5384  Z= 0.365
  Chirality :  0.041   0.161    628
  Planarity :  0.005   0.043    664
  Dihedral  :  4.559  17.369    537
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 33.67 %
    Favored  : 63.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.39), residues: 498
  helix:  1.16 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.39 (0.63), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  94 
 HIS   0.001   0.000   HIS A 348 
 PHE   0.010   0.001   PHE A 411 
 TYR   0.019   0.002   TYR B  12 
 ARG   0.002   0.000   ARG A  48 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  453 TRP cc_start: 0.8210 (m100) cc_final: 0.7388 (m100)
REVERT: A  470 ILE cc_start: 0.8581 (mm) cc_final: 0.8272 (mm)
REVERT: A  474 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7405 (mt-10)
REVERT: A  501 PHE cc_start: 0.8696 (m-80) cc_final: 0.7761 (t80)
REVERT: B   13 TRP cc_start: 0.5706 (OUTLIER) cc_final: 0.5343 (m100)
  outliers start: 12
  outliers final: 11
  residues processed: 124
  average time/residue: 0.1228
  time to fit residues: 19.9940
Evaluate side-chains
  134 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0030
   overall best weight:    0.5790

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.146946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.122166 restraints weight = 7602.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.126053 restraints weight = 4300.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.128724 restraints weight = 2876.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.3671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3955  Z= 0.218
  Angle     :  0.729  12.147   5384  Z= 0.365
  Chirality :  0.041   0.160    628
  Planarity :  0.005   0.043    664
  Dihedral  :  4.514  17.088    537
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 33.92 %
    Favored  : 63.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.38), residues: 498
  helix:  1.13 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -2.38 (0.63), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  13 
 HIS   0.001   0.000   HIS A 348 
 PHE   0.013   0.001   PHE A 411 
 TYR   0.019   0.001   TYR B  12 
 ARG   0.002   0.000   ARG A 426 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8421 (mm-30)
REVERT: A  345 GLN cc_start: 0.8801 (mm110) cc_final: 0.8232 (mm-40)
REVERT: A  426 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8402 (ttp80)
REVERT: A  453 TRP cc_start: 0.8247 (m100) cc_final: 0.7412 (m100)
REVERT: A  470 ILE cc_start: 0.8563 (mm) cc_final: 0.8246 (mm)
REVERT: A  474 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7394 (mt-10)
REVERT: A  501 PHE cc_start: 0.8741 (m-80) cc_final: 0.7760 (t80)
REVERT: B   13 TRP cc_start: 0.5699 (OUTLIER) cc_final: 0.5315 (m100)
  outliers start: 11
  outliers final: 10
  residues processed: 121
  average time/residue: 0.1219
  time to fit residues: 19.3355
Evaluate side-chains
  130 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain B residue   13 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 30 optimal weight:    0.4980
   chunk 28 optimal weight:    0.3980
   chunk 26 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.147490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.123060 restraints weight = 7450.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.126827 restraints weight = 4222.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.129459 restraints weight = 2842.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.3778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3955  Z= 0.215
  Angle     :  0.720  12.593   5384  Z= 0.360
  Chirality :  0.041   0.154    628
  Planarity :  0.005   0.042    664
  Dihedral  :  4.498  16.751    537
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 33.42 %
    Favored  : 63.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.38), residues: 498
  helix:  1.16 (0.26), residues: 398
  sheet:  None (None), residues: 0
  loop : -2.42 (0.64), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  13 
 HIS   0.001   0.000   HIS A 348 
 PHE   0.009   0.001   PHE A 411 
 TYR   0.018   0.001   TYR B  12 
 ARG   0.001   0.000   ARG A 129 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1530.81 seconds
wall clock time: 27 minutes 22.25 seconds (1642.25 seconds total)